Dynamic and electrophoretic light scattering measurements on microtubules at low concentrations.

The accurate characterization of microtubules is essential for understanding their roles in various biological activities in eukaryotic cellular processes. In vitro, experimental data on these systems often need more details and information on sample preparation protocols and experimental techniques. This deficiency leads to unreproducible or contradictory outcomes.

In vitro Preparation of Homogenous Actin Filaments for Dynamic and Electrophoretic Light Scattering Measurements.

Actin filaments are essential for various biological activities in eukaryotic cellular processes. Available in vitro experimental data on these systems often lack details and information on sample preparation protocols and experimental techniques, leading to unreproducible results. Additionally, different experimental techniques and polymerization buffers provide different, sometimes contradictory results on the properties of these systems, making it substantially difficult to gather meaningful data and conclusive information from them.

Characterization of the interaction of metal-protoporphyrins photosensitizers with β- lactoglobulin.

We investigated the interaction of a series of metal-protoporphyrins (PPIXs) with bovine β- lactoglobulin (BLG) using a combination of optical spectroscopy and computational simulations. Unlike other studies, the simulations were not merely used to rationalize the experimental data but were employed to refine the experimental data itself. The study was carried out at two pH values, 5 and 9, where BLG is known to have different conformation dictated by the so-called Tanford transition which occurs near pH 7.

Hydrodynamic and Polyelectrolyte Properties of Actin Filaments: Theory and Experiments.

Actin filament's polyelectrolyte and hydrodynamic properties, their interactions with the biological environment, and external force fields play an essential role in their biological activities in eukaryotic cellular processes. In this article, we introduce a unique approach that combines dynamics and electrophoresis light-scattering experiments, an extended semiflexible worm-like chain model, and an asymmetric polymer length distribution theory to characterize the polyelectrolyte and hydrodynamic properties of actin filaments in aqueous electrolyte solutions. A fitting approach was used to optimize the theories and filament models for hydrodynamic conditions.

A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin. The role of the orientation of the E89 side chain.

molecular dynamics (MD) using crystallographic and NMR data was used to simulate the effects of the protonation state of E89 on the pH-dependent conformational rearrangement of the EF loop, also known as the Tanford transition, in a series of apo-β-lactoglobulin (BLG) structures. Compared to existing studies these simulations were carried out over a much longer time scale (200 ns where the stability of the transition can be evaluated) and used an explicit water model. We considered eight different entries from the Brookhaven Protein Data Bank (PDB) separated into two groups.

Apomyoglobin is an efficient carrier for zinc phthalocyanine in photodynamic therapy of tumors.

The spectral and the photophysical properties of phthalocyanines have made these dyes attractive for applications in photodynamic therapy of cancer. One important known issue of these compounds is their tendency to aggregate in aqueous media, which decreases their fluorescence, triplet, and singlet oxygen quantum yields. We report on the use of apomyoglobin as a carrier for zinc phthalocyanine (ZnPc) to overcome solubility limitations of the dye.

Novel combinations of experimental and computational analysis tested on the binding of metalloprotoporphyrins to albumin.

The evidence that Human Serum Albumin (HSA) binds metal ions and organometallic compounds has generated interest in its physiological role as a metalloprotein and as a vehicle for synthetic biology applications (e.g., synthetic blood and solar energy conversion).

Multi-wavelength analytical ultracentrifugation of human serum albumin complexed with porphyrin.

The new Beckman Coulter Optima AUC instrument, which features multi-wavelength detection that couples the hydrodynamic separation of colloidal mixtures to spectral deconvolution of interacting and non-interacting solutes present in a mixture, was used to analyze the composition of human serum albumin (HSA) bound to metallo-protoporphyrin. We present new methods implemented in UltraScan that permit Optima AUC-derived multi-wavelength data to be spectrally decomposed in the same fashion as has been made possible for the Cölfen detector earlier. We demonstrate this approach by spectrally separating sedimentation velocity experimental data from mixtures of apo-HSA and HSA complexed to different metallo-protoporphyrins.

Experimental and computational characterization of photosensitized conformational effects mediated by protoporphyrin ligands on human serum albumin.

When investigating the interaction between proteins and protoporphyrins in aqueous solution, one typically has to contend with the tendency of the latter to form polydispersed aggregates. The interference of aggregated protoporphyrins manifests, at least, at two levels: aggregates sequester the majority of the protoporphyrin molecules in solution and prevent their interaction with the proteins, but also their presence interferes with optical experiments such as absorption and fluorescence spectroscopy. In this study we present a protocol which uses dialysis and centrifugation to eliminate the aggregates and yield solutions dominated by non-covalent complexes of albumin (HSA) and protoporphyrins.

Human serum albumin as vehicle for the solubilization of perylene diimides in aqueous solutions.

The chemical, physical and photophysical properties of perylene diimides have attracted substantial attention for the potential applications in diverse fields ranging from advanced materials to biomedical applications. Some applications require the diimides to be in aqueous environment where they tend to dissolve poorly. We investigated the use of human serum albumin as a vehicle to increase the aqueous exposure of monomeric perylene diimides.

Effects of Visible-Light Irradiation of Protoporphyrin IX on the Self-Assembly of Tubulin Heterodimers.

The formation and the effects of laser irradiation of the complex formed by protoporphyrin IX (PPIX) and tubulin was investigated. We have used tubulin as a model protein to investigate whether docked photoactive ligands can affect the structure and function of polypeptides upon exposure to visible light. We observed that laser irradiation in the Soret band prompts bleaching of the PPIX, which is accompanied by a sharp decrease in the intensity and average fluorescence lifetime of the protein (dominated by the four tryptophan residues of the tubulin monomer).

Biophysical characterization of the interaction of human albumin with an anionic porphyrin.

The manuscript describes the characterization of the interaction between -tetrakis(-sulfonatophenyl)porphyrin (TSPP) and human serum albumin (HSA). TSPP is a candidate for the photosensitization of structural and functional changes in proteins while HSA provides both an excellent protein model and binding and functional characteristics that could be explored in future applications of the approach. A combination of optical spectroscopic techniques (e.

Partial Unfolding of Tubulin Heterodimers Induced by Two-Photon Excitation of Bound meso-Tetrakis(sulfonatophenyl)porphyrin.

The water-soluble porphyrin meso-tetrakis(p-sulfonatophenyl)porphyrin (TSPP) can be noncovalently bound to tubulin and used as a photosensitizer, which upon irradiation triggers photochemical reactions that lead to conformational changes of the protein. These conformational changes in turn inhibit tubulin's primary function of polymerizing into microtubules. We explored the possibility of using two-photon excitation of the bound porphyrin to induce photosensitized protein unfolding.

Resonance Raman and vibrational mode analysis used to predict ligand geometry for docking simulations of a water soluble porphyrin and tubulin.

The ability to modify the conformation of a protein by controlled partial unfolding may have practical applications such as inhibiting its function or providing non-native photosensitive properties. A water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin (TSPP), non-covalently bound to tubulin can be used as a photosensitizer, which upon irradiation can lead to conformational changes of the protein. To fully understand the mechanism responsible for this partial unfolding and determine the amino acid residues and atoms involved, it is essential to find the most likely binding location and the configuration of the ligand and protein.

Characterization of novel perylene diimides containing aromatic amino acid side chains.

Perylene diimide derivatives have attracted initial interest as industrial dyes. Recently, much attention has been focused on their strong π-π stacks resulting from the large PDI aromatic core. These PDI stacks have distinct optical properties, and provide informative models that could mimic light-harvesting systems and initial charge transfer typical of photosynthetic systems.

The effect of local dynamics of Atto 390-labeled lysozyme on fluorescence anisotropy modeling.

Fluorescence anisotropy decay is a popular optical technique to study the structure, size, shape, and even functions of biomolecules. The method measures the time dependence of the depolarization of a fluorophore and is therefore sensitive to the changes in the rotational motion (e.g.

Porphyrin profile in four human cell lines after supplementation with 5-aminolaevulinic acid and its methyl ester.

Multiple factors can affect the synthesis of the prodrugs aminolaevulinic acid and its methyl ester to protoporphyrin. These may ultimately influence the efficacy of ALA-induced porphyrin as a photosensitiser for photodynamic therapy or fluorescence diagnosis. This study demonstrates the variation in total amount of porphyrin produced and cellular porphyrins synthesised in four different human cell lines after supplementation with these prodrugs.

Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option.

The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state.

Interaction of human serum albumin with novel 3,9-disubstituted perylenes.

Human serum albumin (HSA) has been used as a model for the binding of a number of different ligands, including polyaromatic hydrocarbons, to proteins. In this case we have investigated the interaction of HSA with a novel set of perylene derivatives. Di-substituted perylene analogues have been synthesized as potentially useful organic photovoltaic materials.

Photoinduced partial unfolding of tubulin bound to meso-tetrakis(sulfonatophenyl) porphyrin leads to inhibition of microtubule formation in vitro.

The irradiation of the complex formed by meso-tetrakis (sulfonatophenyl) porphyrin (TSPP) and tubulin was investigated as well as its effects on the structure and function of the protein. We have used tubulin as a model target to investigate whether photoactive ligands docked to the protein can affect the structure and function of the protein upon exposure to visible light. We observed that laser irradiation prompts bleaching of the porphyrin which is accompanied by a sharp decrease (∼2 ns) in the average fluorescence lifetime of the protein and a change in the dichroic spectrum consistent with a decrease of helical structure.

Bovine serum albumin oligomers in the E- and B-forms at low protein concentration and ionic strength.

The manuscript describes the study of the oligomerization process of bovine serum albumin (BSA) in two different structural monomeric forms: the extended-form (E) at pH 2.0 and the basic-form (B) at pH 9.0.

Combination of resonance Raman spectroscopy and docking simulations to study the nonspecific binding of a free-base porphyrin to a globular protein.

Understanding the conformational changes induced by small ligands noncovalently bound to proteins is a central problem in biophysics. We focus on the binding location of the water-soluble porphyrin, meso-tetrakis (p-sulfonatophenyl) porphyrin, to a globular protein, β-lactoglobulin, which has been observed to partially unfold when irradiated by laser light. Identifying the binding location is necessary to determine the mechanism of action as well as the atoms and residues involved in the photoinduced partial unfolding.

Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles.

To probe structural changes that occur when a membrane protein is transferred from lipid bilayers to SDS micelles, a fragment of bacteriorhodopsin containing transmembrane helical segments A and B was studied by fluorescence spectroscopy, molecular dynamics (MD) simulation, and stopped flow kinetics. In lipid bilayers, Förster resonance energy transfer (FRET) was observed between tyrosine 57 on helix B and tryptophans 10 and 12 on helix A. FRET efficiency decreased substantially when the peptide was transferred to SDS.

The photophysical Characterisation of Novel 3,9-Dialkyloxy- and Diacyloxyperylenes.

The fundamental photophysical properties of three symmetrically substituted 3,9-perylene analogues were examined in a diverse range of solvents. All three compounds exhibited solvent-dependent fluorescence quantum yield, which was lower than that of perylene or its diimides. Whilst the absence of a large excited state dipole moment suggests that there is no preferential charge accumulation in one side of the molecules, the data suggest that intramolecular electron transfer occurs and that such an event causes additional photochemical mechanisms in chlorinated compounds where the fluorescence quantum yield is lower than in all other solvents and the values of the fluorescence decay change significantly.

Porphyrins affect the self-assembly of tubulin in solution.

Self-assembly of tubulin heterodimers in solution has been studied in the past to predict the effects that ligands and/or conformational changes have on the formation of tubulin filaments. Self-assembly of tubulin in solution has produced formations similar to cellular microtubules (MTs). The present study reports on the effects that two porphyrins (protoporphyrin IX, PPIX and tetrakis(4-sulfonatophenyl)porphyrin, TPPS) produce on the self-assembly of tubulin alpha,beta-heterodimers in buffer solution.